Just so we're on the same page, I'll mention some stuff you already know. The boiler is short cycling because it puts more heat into the water than can be effectively radiated. The ideal solution is a modulating burner with a wide turn down ratio. Unfortunately retrofitting a modulating burner and it's associated controls is not typically considered to be an economically viable option.
It seems to me that you have two or three choices:
1) Replace current boiler with a mod-con
2) Increase the heat storage capacity of the system
3) Stop using the wood stove when the boiler starts short cycling
Number 1 may not be cost effective.
Number 2 is relatively simple to implement if you've got room for a reverse indirect tank. Basically a water tank is added to the primary loop of the hydronic system so that the boiler heats 10 times (or so) the water volume on each cycle.
Number 3 is obviously not a real effective solution
Maybe a hydronic specialist will have other options.